Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for CANX
Basic gene info.Gene symbolCANX
Gene namecalnexin
SynonymsCNX|IP90|P90
CytomapUCSC genome browser: 5q35
Genomic locationchr5 :179125929-179158639
Type of geneprotein-coding
RefGenesNM_001024649.1,
NM_001746.3,
Ensembl idENSG00000127022
Descriptionmajor histocompatibility complex class I antigen-binding protein p88
Modification date20141207
dbXrefs MIM : 114217
HGNC : HGNC
Ensembl : ENSG00000127022
HPRD : 00252
Vega : OTTHUMG00000130910
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CANX
BioGPS: 821
Gene Expression Atlas: ENSG00000127022
The Human Protein Atlas: ENSG00000127022
PathwayNCI Pathway Interaction Database: CANX
KEGG: CANX
REACTOME: CANX
ConsensusPathDB
Pathway Commons: CANX
MetabolismMetaCyc: CANX
HUMANCyc: CANX
RegulationEnsembl's Regulation: ENSG00000127022
miRBase: chr5 :179,125,929-179,158,639
TargetScan: NM_001024649
cisRED: ENSG00000127022
ContextiHOP: CANX
cancer metabolism search in PubMed: CANX
UCL Cancer Institute: CANX
Assigned class in ccmGDBC

Top
Phenotypic Information for CANX(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CANX
Familial Cancer Database: CANX
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CANX
MedGen: CANX (Human Medical Genetics with Condition)
ClinVar: CANX
PhenotypeMGI: CANX (International Mouse Phenotyping Consortium)
PhenomicDB: CANX

Mutations for CANX
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasCANXchr5179141104179141124chr5179055101179055121
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CANX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N44604CANX12105179156135179156344MLIP20828365398626553986340
BM726297KIFC3169165779233357792401CANX694955179157500179157926
BG168464CANX1845179147429179147512CSDA77307121085169410851923
BM680904CANX194455179157500179157926KIFC3445498165779233357792386
BE150450TGFBR171129101915624101915729CANX1036145179155621179156133
CB242580CANX193765179157569179157926CANX3725485179157392179157568
AL046980RBBP628669162458082024581461CANX6617785179157329179157446
BF949860CALM1278149087296690873043CANX741665179146676179146768
CB856751CANX12695179143186179147449CANX2676245179156065179156422
BG009982CANX62025179155948179156146KDM5B1904591202712054202712323
AW583198CANX241295179156758179156863CANX1303555179156530179156755
AU125279CANX14225179156591179157013SNHG342074712883382028834153
BE836489TMTC12234122972703629727270CANX2313825179136873179137024
BI019346CLSPN129013623015536235467CANX2884065179135979179136910
AW469973CANX13705179157203179157572CANX3675255179157020179157179
CA448313PRSS2318275118651996886520225CANX2755465179156721179156992
BP240903CANX14535179149870179153735PPAP2B45157315704520357045325

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

Top
check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr5:179149920-179149920p.F435fs*124
chr5:179149857-179149857p.E412G3
chr5:179147524-179147524p.K382I2
chr5:179149818-179149818p.P399L2
chr5:179132740-179132740p.A20T2
chr5:179149856-179149856p.E412Q2
chr5:179132741-179132741p.A20V2
chr5:179135268-179135268p.E111D2
chr5:179132699-179132699p.L6S1
chr5:179150687-179150687p.E475D1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 51   4  53   2218
# mutation22 51   4  63   2218
nonsynonymous SNV12 21   4  52   1115
synonymous SNV1  3       11   11 3
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

Top
check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr5:179149818p.P399L,CANX2
chr5:179132689p.H21H,CANX1
chr5:179151779p.A310P,CANX1
chr5:179136958p.D37N,CANX1
chr5:179132699p.D335D,CANX1
chr5:179153702p.D92H,CANX1
chr5:179136977p.R125L,CANX1
chr5:179149917p.D432G,CANX1
chr5:179132703p.N156N,CANX1
chr5:179155595p.G456C,CANX1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for CANX in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

Top
Gene Expression for CANX

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AFF4,CANX,CLINT1,CNOT6,ETF1,FAF2,FBXW11,
HSPA9,LARP1,LMBRD2,LYSMD3,MAPK9,NSD1,RAD50,
RBM27,SEC24A,SLC25A46,SLC30A5,STT3B,TMED7,TTC37
API5,ATP6V1A,CANX,CAPRIN1,COPB1,GOLPH3L,GOSR1,
IMPACT,CFAP97,LMBR1,POC1B,PRRC1,SLC33A1,SLC39A9,
SPIN1,SRP72,TM9SF2,TMED10,TMED2,TMEM181,VPS4B

AP3B1,CANX,CNOT6,DCTN4,DDX46,DNAJC3,ETF1,
FAF2,FBXW11,G3BP1,HSP90B1,LYSMD3,MATR3,MFAP3,
PRRC1,RBM22,RBM27,SLC30A5,SSR3,STT3A,TMED7
ARCN1,CAND1,CANX,CAPRIN1,CCT6A,CPSF2,CSE1L,
GMPS,HNRNPR,HSP90B1,HSPA5,HSPD1,PDIA3,PDIA3P1,
PDIA6,RARS,SSR1,UBQLN1,USO1,XRCC5,ZW10
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for CANX


There's no related Drug.
Top
Cross referenced IDs for CANX
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas